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Articles 1 - 22 of 22
Full-Text Articles in Chemistry
Exploration Of Nucleic Acid Hydrogran Bonding Using Molecular Mechanics And Dft Calculations, Simi Kaur
Exploration Of Nucleic Acid Hydrogran Bonding Using Molecular Mechanics And Dft Calculations, Simi Kaur
Biological Sciences
Many recent theoretical and experimental techniques have been developed to probe the structurefunction relationships of complex biomolecules. The roles of RNAs are dependent upon various intricate structural motifs and interactions, including hairpins, pseudoknots, long range territory contacts, bulges and internal loops, that are not easily captured by these methods. We had previously developed an enhanced replica exchange molecular dynamics method that incorporated secondary structure information in the form of distance restraints in order to effectively overcome kinetic barriers and sample conformational space. In several structures, restrained RNA base pairs near large bulges displayed a preference for stacking over hydrogen bonding …
Fingerprint Analysis: Moving Toward Multiattribute Determination Via Individual Markers, Morgan Eldridge
Fingerprint Analysis: Moving Toward Multiattribute Determination Via Individual Markers, Morgan Eldridge
Chemistry
Forensic science will be forever revolutionized if law enforcement can identify personal attributes of a person of interest solely from a fingerprint. For the past five years, the goal of the Halamek Lab has been to establish a way to identify originator attributes. Specifically, biological sex has been accomplished and the ultimate goal is to continue to accomplish this using a single analyte for each. To date, an enzymatic assay and two chemical assays have been developed for the analysis of multiple analytes. In this thesis, an additional enzymatic assay has been developed. This time, however, the assay utilizes only …
Raman Spectroscopic Examination Of Bloodstains For Forensic Purposes : Background And Race Determination, Ewelina M. Mistek
Raman Spectroscopic Examination Of Bloodstains For Forensic Purposes : Background And Race Determination, Ewelina M. Mistek
Legacy Theses & Dissertations (2009 - 2024)
Chapter 1 of this thesis critically overviews recent developments in forensic trace evidence analysis since 2016. It covers improvements to existing techniques as well as new methods for the analysis of fibers, hair, paint, glass, gunshot residue (GSR), and explosives.
Quantification Of Hemoglobin In Human Blood To Differentiate Individuals From One Another, Audrey Jeanne Auleley
Quantification Of Hemoglobin In Human Blood To Differentiate Individuals From One Another, Audrey Jeanne Auleley
Legacy Theses & Dissertations (2009 - 2024)
Blood is one of the principal sources of evidence in crime scene investigations. The level of hemoglobin in human blood is known to hardly fluctuate over time in a healthy adult patient. Using a method like the sodium lauryl sulfate (SLS) method for hemoglobin level determination is beneficial because SLS converts any other derivates of hemoglobin into methemoglobin. The amount of hemoglobin would be determined using the linear correlation between the absorbance of methemoglobin and its amount in blood samples. Those curves differ significantly from sample to sample. Therefore, a differentiation can be observed between the blood samples of different …
Computational Modeling As A Tool For Designing Ligands And Receptors, Waqas S. Awan
Computational Modeling As A Tool For Designing Ligands And Receptors, Waqas S. Awan
Legacy Theses & Dissertations (2009 - 2024)
Computational methods can be used for a wide range of applications, especially regarding DNA and RNA. Interactions such as sugar torsions, receptor-ligand interactions, ligand docking/drug docking, receptor modeling, and drug design are excellent candidates for computational analysis and in silico experiments. The use of molecular dynamics software (GROMACS) coupled with molecular design software (MOE) produce insights that may have been otherwise difficult to assess. All these problems are academic in nature but have practical uses outside of academia. Understanding alternate linkages can lead to antibiotic assays to address potential superbug epidemics. Modeling DNA superstructures can provide insight into how large …
Evaluation Of Fingerprint Content For Forensic Crime Scene Analysis And Drug Metabolite Detection, Erica Kathryn Brunelle
Evaluation Of Fingerprint Content For Forensic Crime Scene Analysis And Drug Metabolite Detection, Erica Kathryn Brunelle
Legacy Theses & Dissertations (2009 - 2024)
With respect to criminal investigations, one key piece of evidence that often gets overlooked are fingerprints. For years, fingerprint samples have been believed to be useful only for matching purposes using their unique ridges, shapes, and sizes. With the rapid growth of forensic science, it has become evident that the development of fingerprint analysis has been stagnant. The traditional approach has been advantageous for the identification of many individuals; however, many fingerprint samples have been labeled “unusable” due to smudging, smearing, or any one of a myriad of reasons that could cause inconclusive matches. These samples can, however, still be …
Permanently Heated Micro-Wire Electrodes For Electrochemistry Above The Boiling Point, Zhihua Chang
Permanently Heated Micro-Wire Electrodes For Electrochemistry Above The Boiling Point, Zhihua Chang
Legacy Theses & Dissertations (2009 - 2024)
Heated micro-wire electrodes offer lots of advantages, such as, accurate temperature control, enhanced diffusion and accelerated reaction kinetics through micro-stirring effect, easy cleaning, and low cost, etc. Its application in high temperature electrochemistry has gained lots of interests since its debut in the mid-1990s. A maximum of 250 °C has been reported using heating pulses in duration of 5 ms. For various applications, permanently heating would be more useful. In this study, two types of micro-wire electrodes were successfully developed for electrochemistry above the boiling point with acetaminophen as model compound and a continuous heating time of at least 2 …
Saliva As A Diagnostic Biological Fluid And The Human Salivary Proteome, Jessica Ghassan Emsies
Saliva As A Diagnostic Biological Fluid And The Human Salivary Proteome, Jessica Ghassan Emsies
Legacy Theses & Dissertations (2009 - 2024)
Saliva is a unique biologic fluid that contains a varying spectrum of proteins, nucleic acids, electrolytes, and hormones.31 It is an exocrine secretion of the salivary glands which is hypotonic in nature with a pH of 7.2-7.4.31 Saliva plays an important role in the oral cavity.33 It lubricates, hydrates, and bathes the oral cavity, therefore, aiding speech and mastication.33 Saliva forms a barrier on the teeth, protects against demineralization, and aids in remineralization.33 Saliva is required for chewing and food bolus preparation, it contains enzymes necessary for digestion, and mediates the sense of taste.33 It also helps wound healing and …
Development Of Laser Ablation Direct Analysis In Real Time Imaging-Mass Spectrometry (Ladi-Ms)-Applications To Questions Of Relevance To Forensic Science And Plant Biochemistry, Kristen Leigh Fowble
Development Of Laser Ablation Direct Analysis In Real Time Imaging-Mass Spectrometry (Ladi-Ms)-Applications To Questions Of Relevance To Forensic Science And Plant Biochemistry, Kristen Leigh Fowble
Legacy Theses & Dissertations (2009 - 2024)
Methods for the accomplishment of small molecule imaging by mass spectrometry are challenged by the need for sample pre-treatment steps such as cryo-sectioning, dehydration, chemical fixation, or application of a matrix or solvent, that must be performed to obtain interpretable spatial distribution data. Furthermore, these steps along with requirements of the mass analyzer such as high vacuum, can severely limit the range of sample types that can be analyzed by this powerful method. Here, we report the development of a laser ablation-direct analysis in real time imaging-mass spectrometry (LADI-MS) approach which couples a 213 nm Nd:YAG solid state UV laser …
Study Of Small Molecules With Dna Monolayers On Gold Electrodes Using Electrochemical Quartz Crystal Microbalance On The Millisecond Timescale, Sarasi Kaushalya Kumari Galagedera
Study Of Small Molecules With Dna Monolayers On Gold Electrodes Using Electrochemical Quartz Crystal Microbalance On The Millisecond Timescale, Sarasi Kaushalya Kumari Galagedera
Legacy Theses & Dissertations (2009 - 2024)
Biosensors based on DNA self-assembled monolayers (SAMs) combined with electrochemical transducers have shown great potential to serve an important role in simple, accurate and inexpensive genetic analyses relevant to many fields. The most popularly adapted method in designing biosensing platforms is the self-assembly of 5’-alkylthiol-modified single stranded or double stranded DNA on gold surfaces followed by a passivation step using a diluent like mercaptohexanol (MCH). Since analytical performance (sensitivity, selectivity and stability) of such sensors is solely related to the probe surface architecture, methods to characterize and measure the surface density has gained a lot of interest among the scientific …
Defining And Harnessing Nature's Selection Of Geranylation In Rna Modification, Phensinee Haruehanroengra
Defining And Harnessing Nature's Selection Of Geranylation In Rna Modification, Phensinee Haruehanroengra
Legacy Theses & Dissertations (2009 - 2024)
Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. Geranylated-2-thiouridine is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, namely E. coli, E. aerogenes, P. aeruginosa and S. typhimurium by Liu group. It has been found as a post-transcription modification on the wobble position of anticodon of tRNAs specific for glutamic acid, glutamine and lysine. Geranylated-tRNA was shown to correct the frameshifting during the translation of E. coli. However, the reason of the existing of the modification is still largely unclear. To understand why nature incorporates such a hydrophobic group in …
Chemical Enhancement Of Thrombin Binding Aptamer (Tba), Goh Woon Lee
Chemical Enhancement Of Thrombin Binding Aptamer (Tba), Goh Woon Lee
Legacy Theses & Dissertations (2009 - 2024)
The Thrombin Binding Aptamer (TBA), a short DNA strand with G-quadruplex conformation, binds to Thrombin with high affinity and acts as an inhibitor in the blood clotting. The TBA folds into a G-quadruplex conformation and stabilize the binding toward Thrombin. With this specificity of TBA with Thrombin, our goal is to enhance the binding affinity between them to observe the possibility of developing a new anticoagulant. First modification that we studied was dendrimer linkers which are called Trebler (T) and Long Trebler (LT). Those linkers were incorporated at the 5’ end of TBA by using solid phase oligonucleotide synthesis. Second …
Novel Mass Spectrometric Approaches For Deciphering The Epitranscriptomic Code, William D. Mcintyre
Novel Mass Spectrometric Approaches For Deciphering The Epitranscriptomic Code, William D. Mcintyre
Legacy Theses & Dissertations (2009 - 2024)
According to the results of the Human Genome Project, less than 5% of our genome consists of sequences that code for actual proteins. At the same time, however, ~90% of these non-coding sequences are transcribed into a myriad of classes of ribonucleic acids collectively known as ncRNAs, which have been recognized as essential regulatory factors. It has been recently shown that the activity of ncRNAs can be in turn modulated by post-transcriptional modifications (PTMs), covalent marks that can be established/removed by tightly regulated enzymatic pathways. Now, the race is on to understand the new set of controls of cellular functions …
Legislation To Reduce Microplastic Pollution : Understanding The Factors That Facilitated Passage Of The Federal Microbead-Free Waters Act Of 2015, Alyson Kelly Northrup
Legislation To Reduce Microplastic Pollution : Understanding The Factors That Facilitated Passage Of The Federal Microbead-Free Waters Act Of 2015, Alyson Kelly Northrup
Legacy Theses & Dissertations (2009 - 2024)
The full environmental impacts of microplastic pollution in aquatic environments remain uncertain, but several detrimental effects have been documented, including adverse health effects in multiple species and the susceptibility of microplastics to adsorb toxins and leach plastic additives. Plastic microbeads from rinse-off personal care products are a source of microplastic pollution that is introduced directly into the environment through runoff, including wastewater treatment plant effluent. In December 2015, the federal Microbead-free Waters Act of 2015 banned the manufacture and sale of all rinse-off personal care products containing plastic microbeads in the United States.
Synthesis Of Cadmium Arsenide Semiconductor Nanoparticles, Superatomic Silver Clusters, And Silver Coordination Polymers, Sarthak Jashubhai Patel
Synthesis Of Cadmium Arsenide Semiconductor Nanoparticles, Superatomic Silver Clusters, And Silver Coordination Polymers, Sarthak Jashubhai Patel
Legacy Theses & Dissertations (2009 - 2024)
Nanomaterials have chemical, electronic, optical, and other properties distinct from their bulk counterparts. However, the atom-precise synthesis of these materials remains a challenge, leaving open many scientific questions regarding the size regime between nanoparticulate (quantum confined) and bulk character. In this work, efforts toward the synthesis of nanoparticulate and atom-precise metal and semimetal materials are described. The synthesis of II-V semiconductor Cd3As2 having a near-zero bandgap is discussed. Analysis by UV-Vis absorption spectroscopy and powder X-ray diffraction indicate the formation of material with unexpected crystallinity and absorption properties The interaction between the molecular source of As and the solvent was …
Modeling Chaperone-Substrate Interactions Of Alpha Crystallin From The Ocular Lens, Lisa Marie S. Ramirez
Modeling Chaperone-Substrate Interactions Of Alpha Crystallin From The Ocular Lens, Lisa Marie S. Ramirez
Legacy Theses & Dissertations (2009 - 2024)
The α-crystallins (αA- and αB-crystallin isoforms) from the ocular lens are small heat shock proteins and molecular chaperones, widely believed to play a significant role in protecting the lens from cataract. Mutations and modifications on human αA- and αB-crystallin (HAA and HAB, respectively) are linked to a variety of diseases, including cataract formation, neuropathological protein folding disorders, and many others. It is believed that HAA and HAB prevent the aggregation of other lens proteins. However, the structural and thermodynamic details of the chaperone-substrate (aka “client”) interaction are sparse. Therefore, the main objective of this dissertation is to reveal structural and …
Protein Ligation : Selenocysteine, Komal Shah
Protein Ligation : Selenocysteine, Komal Shah
Legacy Theses & Dissertations (2009 - 2024)
Selenium is present in human and animal body in the form of selenocysteine and
Accumulation And Spatial Distribution Of Lead And Other Trace Elements In Keratinized Tissues : Investigations Based On Analytical Atomic Spectrometry, Mina W. Tehrani
Accumulation And Spatial Distribution Of Lead And Other Trace Elements In Keratinized Tissues : Investigations Based On Analytical Atomic Spectrometry, Mina W. Tehrani
Legacy Theses & Dissertations (2009 - 2024)
Human biomonitoring for toxic metals such as lead (Pb) provides information about absorbed dose from all exposure routes, and is critical for identifying exposed individuals and assessing health risks. Blood Pb and bone Pb are the primary validated biomarkers for assessing short-term and historical Pb exposures, respectively, while non-traditional matrices, including keratinized tissues, can provide complementary exposure information. Hard keratinized tissues – including hair, nails, hooves, and horns – grow incrementally, potentially preserving chemical exposure histories over a span of days to years. Analytical limitations and poor interlaboratory reproducibility, however, have led to debate around the use of human nails …
Characterization Of Ambient Aerosols And Their Evolution Under Various Atmospheric Conditions In The Northeast U.S, Jie Zhang
Legacy Theses & Dissertations (2009 - 2024)
The University at Albany Atmospheric Sciences Research Center (ASRC) mobile laboratory, which includes a High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS), a Scanning Mobility Particle Sizer (SMPS), and several gas sensors, etc., has been used to characterize atmospheric aerosols and air quality at different locations in the Northeastern US (including urban, forest, and mountain areas) and the aerosol evolutions under a variety of atmospheric conditions (including extreme weather, fog, and cloud, etc.). In this dissertation, I present the findings of the several field measurements using the ASRC mobile lab, focusing on the influences of extreme events (including high O3, heatwave, …
Sers For Protein Detection At A Single Molecule Level For Developing A New Medical Diagnostics Platform, Lamyaa Almehmadi
Sers For Protein Detection At A Single Molecule Level For Developing A New Medical Diagnostics Platform, Lamyaa Almehmadi
Legacy Theses & Dissertations (2009 - 2024)
A two-step process of protein detection at a single molecule level using Surface Enhanced Raman Spectroscopy (SERS) was developed as a new platform for medical diagnostics in this proof-of-concept study. First, a protein molecule was bound to a linker in the bulk solution and then this adduct was chemically reacted with the SERS substrate. Traut’s Reagent (TR) was used to thiolate Bovine serum albumin (BSA) in solution followed by chemical cross linking to a gold surface through a sulfhydryl group. A Glycine-TR adduct was used as a control sample to identify the protein contribution to the SER spectra. Gold SERS …
Characterizing Body Fluids With Raman Spectroscopy : Towards Real World Application, Marisia Ann Fikiet
Characterizing Body Fluids With Raman Spectroscopy : Towards Real World Application, Marisia Ann Fikiet
Legacy Theses & Dissertations (2009 - 2024)
This project continues the research on a new method of body fluid identification and furthers its field capabilities. This method of identification uses Raman spectroscopy and advanced chemometrics to distinguish between body fluids. It is an improvement on current methods because it is confirmatory, non-destructive, and has simple sample preparation. The first objective of this research is to create a model for differentiating body fluids for a new desktop instrument. It was determined that due to resolution differences from a research grade instrument, a new model needed to be made for this the desktop instrument. This model will be able …
Synthesis And Adsorption Experiments With Metal-Organic Frameworks For High School And Undergraduate Laboratory Settings, Kate Holley
Legacy Theses & Dissertations (2009 - 2024)
Seven experiments are described and outlined here that introduce high school and undergraduate students to metal–organic frameworks (MOFs) and their applications. The experiments were designed to be completed with basic laboratory equipment and supplies and without the use of expensive characterization instruments, simulating typical high school chemistry laboratory conditions. Students synthesized two well-known MOFs, HKUST-1 and aluminum fumarate, using simple, safe, and rapid methods (fast enough to be performed within the time constrains of a typical high school class). Students then use their synthesized MOFs to explore their inherent sorption properties. In one set of experiments, the synthesized MOFs are …